diff --git a/EDAM_dev.owl b/EDAM_dev.owl index 9446832..a5225c7 100644 --- a/EDAM_dev.owl +++ b/EDAM_dev.owl @@ -45,13 +45,13 @@ 12.05.2016 18:23 GMT EDAM_data http://edamontology.org/data_ "EDAM types of data" concept_properties "EDAM concept properties" + 3766 + EDAM is an ontology of well established, familiar concepts that are prevalent within bioinformatics, including types of data and data identifiers, data formats, operations and topics. EDAM is a simple ontology - essentially a set of terms with synonyms and definitions - organised into an intuitive hierarchy for convenient use by curators, software developers and end-users. EDAM is suitable for large-scale semantic annotations and categorisation of diverse bioinformatics resources. EDAM is also suitable for diverse application including for example within workbenches and workflow-management systems, software distributions, and resource registries. Jon Ison Matúš Kalaš EDAM_format http://edamontology.org/format_ "EDAM data formats" - 3751 topics "EDAM topics" Hervé Ménager - EDAM is an ontology of well established, familiar concepts that are prevalent within bioinformatics, including types of data and data identifiers, data formats, operations and topics. EDAM is a simple ontology - essentially a set of terms with synonyms and definitions - organised into an intuitive hierarchy for convenient use by curators, software developers and end-users. EDAM is suitable for large-scale semantic annotations and categorization of diverse bioinformatics resources. EDAM is also suitable for diverse application including for example within workbenches and workflow-management systems, software distributions, and resource registries. 1.16_dev @@ -418,16 +418,16 @@ - OBO_REL:bearer_of - Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:bearer_of' is narrower in the sense that it only relates ontological categories (concepts) that are an 'independent_continuant' (snap:IndependentContinuant) with ontological categories that are a 'specifically_dependent_continuant' (snap:SpecificallyDependentContinuant), and broader in the sense that it relates with any borne objects not just functions of the subject. + true + In very unusual cases. - + - In very unusual cases. - true + OBO_REL:bearer_of + Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:bearer_of' is narrower in the sense that it only relates ontological categories (concepts) that are an 'independent_continuant' (snap:IndependentContinuant) with ontological categories that are a 'specifically_dependent_continuant' (snap:SpecificallyDependentContinuant), and broader in the sense that it relates with any borne objects not just functions of the subject. - + @@ -505,16 +505,16 @@ - In very unusual cases. - true + OBO_REL:has_participant + 'OBO_REL:has_participant' is narrower in the sense that it only relates ontological categories (concepts) that are a 'process' (span:Process) with ontological categories that are a 'continuant' (snap:Continuant), and broader in the sense that it relates with any participating objects not just outputs or output arguments of the subject. It is also not clear whether an output (result) actually participates in the process that generates it. - + - 'OBO_REL:has_participant' is narrower in the sense that it only relates ontological categories (concepts) that are a 'process' (span:Process) with ontological categories that are a 'continuant' (snap:Continuant), and broader in the sense that it relates with any participating objects not just outputs or output arguments of the subject. It is also not clear whether an output (result) actually participates in the process that generates it. - OBO_REL:has_participant + true + In very unusual cases. - + @@ -547,8 +547,8 @@ - In very unusual cases. true + In very unusual cases. @@ -575,8 +575,8 @@ - Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:quality_of' might be seen narrower in the sense that it only relates subjects that are a 'quality' (snap:Quality) with objects that are an 'independent_continuant' (snap:IndependentContinuant), and is broader in the sense that it relates any qualities of the object. OBO_REL:quality_of + Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:quality_of' might be seen narrower in the sense that it only relates subjects that are a 'quality' (snap:Quality) with objects that are an 'independent_continuant' (snap:IndependentContinuant), and is broader in the sense that it relates any qualities of the object. @@ -604,20 +604,20 @@ - true - In very unusual cases. - - - - OBO_REL:function_of Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:function_of' only relates subjects that are a 'function' (snap:Function) with objects that are an 'independent_continuant' (snap:IndependentContinuant), so for example no processes. It does not define explicitly that the subject is a function of the object. - OBO_REL:inheres_in + true + In very unusual cases. + + + + Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:inheres_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'specifically_dependent_continuant' (snap:SpecificallyDependentContinuant) with ontological categories that are an 'independent_continuant' (snap:IndependentContinuant), and broader in the sense that it relates any borne subjects not just functions. + OBO_REL:inheres_in @@ -665,16 +665,16 @@ - 'OBO_REL:participates_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'continuant' (snap:Continuant) with ontological categories that are a 'process' (span:Process), and broader in the sense that it relates any participating subjects not just inputs or input arguments. - OBO_REL:participates_in + In very unusual cases. + true - + - true - In very unusual cases. + 'OBO_REL:participates_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'continuant' (snap:Continuant) with ontological categories that are a 'process' (span:Process), and broader in the sense that it relates any participating subjects not just inputs or input arguments. + OBO_REL:participates_in - + @@ -700,16 +700,16 @@ - 'OBO_REL:participates_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'continuant' (snap:Continuant) with ontological categories that are a 'process' (span:Process), and broader in the sense that it relates any participating subjects not just outputs or output arguments. It is also not clear whether an output (result) actually participates in the process that generates it. - OBO_REL:participates_in + In very unusual cases. + true - + - true - In very unusual cases. + OBO_REL:participates_in + 'OBO_REL:participates_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'continuant' (snap:Continuant) with ontological categories that are a 'process' (span:Process), and broader in the sense that it relates any participating subjects not just outputs or output arguments. It is also not clear whether an output (result) actually participates in the process that generates it. - + @@ -747,8 +747,8 @@ - true In very unusual cases. + true @@ -806,14 +806,8 @@ - EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set). Data set - - - - EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set). - Datum @@ -823,6 +817,12 @@ + + Datum + EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set). + + + @@ -1884,7 +1884,7 @@ Protein folding report beta12orEarlier - A report on an analysis or model of protein folding properties, folding pathways, residues or sites that are key to protein folding, nucleation or stabilization centers etc. + A report on an analysis or model of protein folding properties, folding pathways, residues or sites that are key to protein folding, nucleation or stabilisation centers etc. true 1.8 @@ -2135,9 +2135,9 @@ Nucleic acid features report (primers) true + PCR primers and hybridisation oligos in a nucleic acid sequence. 1.8 beta12orEarlier - PCR primers and hybridization oligos in a nucleic acid sequence. @@ -2190,8 +2190,8 @@ - SO:0001248 Perhaps surprisingly, the definition of 'SO:assembly' is narrower than the 'SO:sequence_assembly'. + SO:0001248 @@ -3277,9 +3277,9 @@ Chemical name (INN) + International Non-proprietary Name (INN or 'generic name') of a chemical compound, assigned by the World Health Organisation (WHO). INN chemical name beta12orEarlier - International Non-proprietary Name (INN or 'generic name') of a chemical compound, assigned by the World Health Organization (WHO). @@ -4545,13 +4545,13 @@ - + - + Unique name of a codon usage table. @@ -6635,9 +6635,9 @@ Primer3 internal oligo mishybridizing library + A library of nucleotide sequences to avoid during hybridisation events. Hybridisation of the internal oligo to sequences in this library is avoided, rather than priming from them. The file is in a restricted FASTA format. true beta12orEarlier - A library of nucleotide sequences to avoid during hybridization events. Hybridization of the internal oligo to sequences in this library is avoided, rather than priming from them. The file is in a restricted FASTA format. beta12orEarlier @@ -7329,9 +7329,9 @@ Sequence features (repeats) beta12orEarlier + The report might include derived data map such as classification, annotation, organisation, periodicity etc. true 1.5 - The report might include derived data map such as classification, annotation, organization, periodicity etc. Location of short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences. @@ -8363,7 +8363,7 @@ Alignment score or penalty - + beta12orEarlier A simple floating point number defining the penalty for opening or extending a gap in an alignment. @@ -9937,13 +9937,13 @@ - Protein subcellular localization + Protein subcellular localisation - Protein report (subcellular localization) - An informative report on protein subcellular localization (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or destination (exported / extracellular proteins). + Protein report (subcellular localisation) beta12orEarlier true beta13 + An informative report on protein subcellular localisation (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or destination (exported / extracellular proteins). @@ -14729,7 +14729,7 @@ - Protein ionization curve + Protein ionisation curve beta12orEarlier @@ -16852,16 +16852,13 @@ Parameter - - http://semanticscience.org/resource/SIO_000144 - Tool-specific parameter + beta12orEarlier - http://www.e-lico.eu/ontologies/dmo/DMOP/DMOP.owl#Parameter + 1.16 Typically a simple numerical or string value that controls the operation of a tool. - Tool parameter - Parameters - - + true + + @@ -16946,7 +16943,7 @@ Sequence attribute - + An attribute of a molecular sequence, possibly in reference to some other sequence. Sequence parameter beta12orEarlier @@ -20395,13 +20392,13 @@ - + - + Identifier of a lipid. @@ -21325,7 +21322,7 @@ Sequence features metadata - + beta12orEarlier Metadata on sequence features. @@ -21821,7 +21818,7 @@ Pathway or network report - + @@ -23658,7 +23655,6 @@ Text - Any free or plain text, as often specified as some search query. Plain text Free text @@ -23939,6 +23935,90 @@ + + + + Enrichment report + + + + + + + + 1.16 + An informative report containing a ranked list of ontology terms each associated with a statistical metric, concerning or derived from the analysis of a set of identifiers. + + + + + + + + + + GO term enrichment report + + + + + + + + An informative report containing a ranked list of gene ontology terms each associated with a p-value, concerning or derived from the analysis of a set of gene or protein identifiers. + GO term report + Gene ontology enrichment report + 1.16 + + + + + + + + + + Localisation score + + PTM localisation + Score for localization of one or more post-translational modifications in peptide sequence measured by mass spectrometry. + False localisation rate + 1.16 + PTM score + + + + + + + + + + Unimod ID + + 1.16 + Identifier of a protein modification catalogued in the Unimod database. + + + + + + + + + + + ProteomeXchange ID + + Identifier for mass spectrometry proteomics data in the proteomexchange.org repository. + 1.16 + + + + + + + @@ -25735,8 +25815,8 @@ Primer3 primer - Report format on PCR primers and hybridization oligos as generated by Whitehead primer3 program. beta12orEarlier + Report format on PCR primers and hybridisation oligos as generated by Whitehead primer3 program. @@ -26569,16 +26649,16 @@ - File format - File format denotes only formats of a computer file, but the same formats apply also to data blobs or exchanged messages. + Data model + A defined data format has its implicit or explicit data model, and EDAM does not distinguish the two. Some data models however do not have any standard way of serialisation into an exchange format, and those are thus not considered formats in EDAM. (Remark: even broader - or closely related - term to 'Data model' would be an 'Information model'.) - + - A defined data format has its implicit or explicit data model, and EDAM does not distinguish the two. Some data models however do not have any standard way of serialisation into an exchange format, and those are thus not considered formats in EDAM. (Remark: even broader - or closely related - term to 'Data model' would be an 'Information model'.) - Data model + File format + File format denotes only formats of a computer file, but the same formats apply also to data blobs or exchanged messages. - + @@ -28396,8 +28476,8 @@ Nucleic acid features (primers) format + Format of a report on PCR primers or hybridisation oligos in a nucleic acid sequence. beta12orEarlier - Format of a report on PCR primers or hybridization oligos in a nucleic acid sequence. @@ -28598,13 +28678,13 @@ - + - + Data format for the emission and transition counts of a hidden Markov model. @@ -29424,13 +29504,13 @@ - + - + BioXSD XML format @@ -30912,9 +30992,9 @@ Turtle + The Terse RDF Triple Language (Turtle) is a human-friendly serialisation format for RDF (Resource Description Framework) graphs. The SPARQL Query Language incorporates a very similar syntax. 1.2 - The Terse RDF Triple Language (Turtle) is a human-friendly serialization format for RDF (Resource Description Framework) graphs. @@ -30942,8 +31022,8 @@ Notation3 + A shorthand non-XML serialisation of Resource Description Framework model, designed with human-readability in mind. N3 - A shorthand non-XML serialization of Resource Description Framework model, designed with human-readability in mind. @@ -30959,7 +31039,7 @@ Resource Description Framework (RDF) XML format. 1.2 http://www.ebi.ac.uk/SWO/data/SWO_3000006 - RDF/XML is a serialization syntax for OWL DL, but not for OWL Full. + RDF/XML is a serialisation syntax for OWL DL, but not for OWL Full. @@ -31593,7 +31673,7 @@ 1.9 - Nearly Raw Rasta Data format designed to support scientific visualization and image processing involving N-dimensional raster data. + Nearly Raw Rasta Data format designed to support scientific visualisation and image processing involving N-dimensional raster data. @@ -32503,7 +32583,7 @@ Open data format for the storage, exchange, and processing of peptide sequence assignments of MS/MS scans, intended to provide a common data output format for many different MS/MS search engines and subsequent peptide-level analyses. 1.12 - + @@ -33150,11 +33230,11 @@ experiments employing a combination of technologies. YAML - YAML (YAML Ain't Markup Language) is a human-readable tree-structured data serialization language. YAML version 1.2 is a superset of JSON; prior versions were "not strictly compatible". Data in YAML format can be serialised into text, or binary format. 1.15 YAML Ain't Markup Language + YAML (YAML Ain't Markup Language) is a human-readable tree-structured data serialisation language. yaml|yml @@ -33197,6 +33277,48 @@ experiments employing a combination of technologies. + + + + SEQUEST .out file + + + 1.16 + "Raw" result file from SEQUEST database search. + + + + + + + + + + idXML + + + XML file format for files containing information about peptide identifications from mass spectrometry data analysis carried out with OpenMS. + 1.16 + http://open-ms.sourceforge.net/schemas/ + + + + + + + + + + KNIME datatable format + + 1.16 + Data table formatted such that it can be passed/streamed within the KNIME platform. + + + + + + @@ -33240,6 +33362,12 @@ experiments employing a combination of technologies. + Operation is a function that is computational. It typically has input(s) and output(s), which are always data. + Function + + + + Process can have a function (as its quality/attribute), and can also perform an operation with inputs and outputs. Process @@ -33251,12 +33379,6 @@ experiments employing a combination of technologies. - - Operation is a function that is computational. It typically has input(s) and output(s), which are always data. - Function - - - @@ -33309,14 +33431,14 @@ experiments employing a combination of technologies. - - + + - - + + Annotate an entity (typically a biological or biomedical database entity) with terms from a controlled vocabulary. @@ -33471,14 +33593,14 @@ experiments employing a combination of technologies. - - + + - - + + Calculate sequence ambiguity, for example identity regions in protein or nucleotide sequences with many ambiguity codes. @@ -33543,14 +33665,14 @@ experiments employing a combination of technologies. - - + + - - + + Motifs and patterns might be conserved or over-represented (occur with improbable frequency). @@ -33571,14 +33693,14 @@ experiments employing a combination of technologies. - - + + - - + + beta12orEarlier @@ -33606,14 +33728,14 @@ experiments employing a combination of technologies. - - + + - - + + beta12orEarlier @@ -33663,14 +33785,14 @@ experiments employing a combination of technologies. - - + + - - + + This might be a residue-level search for properties such as solvent accessibility, hydropathy, secondary structure, ligand-binding etc. @@ -33832,14 +33954,14 @@ experiments employing a combination of technologies. - - + + - - + + Immunogenicity prediction @@ -33923,20 +34045,20 @@ experiments employing a combination of technologies. - - + + - + - - + + beta12orEarlier @@ -34227,14 +34349,14 @@ experiments employing a combination of technologies. - - + + - - + + Analyse experimental protein-protein interaction data from for example yeast two-hybrid analysis, protein microarrays, immunoaffinity chromatography followed by mass spectrometry, phage display etc. @@ -34406,8 +34528,8 @@ experiments employing a combination of technologies. beta12orEarlier QTL mapping - This includes mapping of the genetic architecture of dynamic complex traits (functional mapping), e.g. by characterization of the underlying quantitative trait loci (QTLs) or nucleotides (QTNs). Linkage mapping + This includes mapping of the genetic architecture of dynamic complex traits (functional mapping), e.g. by characterisation of the underlying quantitative trait loci (QTLs) or nucleotides (QTNs). Genetic map generation Mapping involves ordering genetic loci along a chromosome and estimating the physical distance between loci. A genetic map shows the relative (not physical) position of known genes and genetic markers. Generate a genetic (linkage) map of a DNA sequence (typically a chromosome) showing the relative positions of genetic markers based on estimation of non-physical distances. @@ -34487,32 +34609,32 @@ experiments employing a combination of technologies. - - + + - + - - + + - - + + - - + + beta12orEarlier @@ -34533,14 +34655,14 @@ experiments employing a combination of technologies. - - + + - - + + Identify and plot third base position variability in a nucleotide sequence. @@ -34720,20 +34842,20 @@ experiments employing a combination of technologies. - - + + - - + + - - + + Sequence profile construction @@ -34754,19 +34876,19 @@ experiments employing a combination of technologies. - + - - + + - - + + Structural profile generation @@ -34792,14 +34914,14 @@ experiments employing a combination of technologies. - - + + - - + + Sequence profile alignment @@ -34820,14 +34942,14 @@ experiments employing a combination of technologies. - - + + - - + + Structural profile alignment @@ -34854,14 +34976,14 @@ experiments employing a combination of technologies. - - + + - - + + beta12orEarlier @@ -34882,14 +35004,14 @@ experiments employing a combination of technologies. - - + + - - + + beta12orEarlier @@ -34910,14 +35032,14 @@ experiments employing a combination of technologies. - - + + - - + + beta12orEarlier @@ -35003,12 +35125,6 @@ experiments employing a combination of technologies. - - - - - - @@ -35019,6 +35135,12 @@ experiments employing a combination of technologies. + + + + + + Text data mining beta12orEarlier Process and analyse text (typically the biomedical and informatics literature) to extract information from it. @@ -35054,12 +35176,6 @@ experiments employing a combination of technologies. - - - - - - @@ -35070,6 +35186,12 @@ experiments employing a combination of technologies. + + + + + + This includes predicting primers based on gene structure, promoters, exon-exon junctions, predicting primers that are conserved across multiple genomes or species, primers for for gene transcription profiling, for genotyping polymorphisms, for example single nucleotide polymorphisms (SNPs), for large scale sequencing, or for methylation PCRs. PCR primer design (based on gene structure) PCR primer design (for methylation PCRs) @@ -35095,26 +35217,26 @@ experiments employing a combination of technologies. - - + + - - + + - - + + - + Predict and/or optimize oligonucleotide probes for DNA microarrays, for example for transcription profiling of genes, or for genomes and gene families. @@ -35134,14 +35256,14 @@ experiments employing a combination of technologies. - - + + - - + + beta12orEarlier @@ -35156,18 +35278,18 @@ experiments employing a combination of technologies. - Microarray data standardization and normalization + Microarray data standardisation and normalisation - + - + @@ -35342,14 +35464,14 @@ experiments employing a combination of technologies. - - + + - - + + beta12orEarlier @@ -35368,14 +35490,14 @@ experiments employing a combination of technologies. - - + + - - + + WHATIF: UseResidueDB @@ -35480,13 +35602,13 @@ experiments employing a combination of technologies. - + - + @@ -35612,14 +35734,14 @@ experiments employing a combination of technologies. - - + + - - + + Predict and optimise zinc finger protein domains for DNA/RNA binding (for example for transcription factors and nucleases). @@ -35694,14 +35816,14 @@ experiments employing a combination of technologies. - - + + - - + + @@ -35710,7 +35832,6 @@ experiments employing a combination of technologies. - Visualization beta12orEarlier Visualise, plot or render (graphically) biomolecular data such as molecular sequences or structures. Rendering @@ -36196,7 +36317,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Sequence mutation and randomization + Sequence mutation and randomisation beta12orEarlier Mutate a molecular sequence a specified amount or shuffle it to produce a randomized sequence with the same overall composition. @@ -36334,8 +36455,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Repeat sequence organisation analysis + Analyse repeat sequence organisation such as periodicity. beta12orEarlier - Analyse repeat sequence organization such as periodicity. @@ -36677,14 +36798,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Calculate pH-dependent properties from pKa calculations of a protein sequence. @@ -36884,7 +37005,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein signal peptide detection (eukaryotes) beta12orEarlier - Detect or predict signal peptides (and typically predict subcellular localization) of eukaryotic proteins. + Detect or predict signal peptides (and typically predict subcellular localisation) of eukaryotic proteins. @@ -36896,7 +37017,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein signal peptide detection (bacteria) - Detect or predict signal peptides (and typically predict subcellular localization) of bacterial proteins. + Detect or predict signal peptides (and typically predict subcellular localisation) of bacterial proteins. beta12orEarlier @@ -37062,7 +37183,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein folding site prediction - Predict protein sites that are key to protein folding, such as possible sites of nucleation or stabilization. + Predict protein sites that are key to protein folding, such as possible sites of nucleation or stabilisation. beta12orEarlier @@ -37952,9 +38073,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Comparative modelling + The model might be of a whole, part or aspect of protein structure. Molecular modelling methods might use sequence-structure alignment, structural templates, molecular dynamics, energy minimisation etc. beta12orEarlier Build a three-dimensional protein model based on known (for example homologs) structures. - The model might be of a whole, part or aspect of protein structure. Molecular modelling methods might use sequence-structure alignment, structural templates, molecular dynamics, energy minimization etc. Homology modelling Homology structure modelling Protein structure comparative modelling @@ -38127,9 +38248,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern beta12orEarlier true - This can involve characterization of the underlying quantitative trait loci (QTLs) or nucleotides (QTNs). Map the genetic architecture of dynamic complex traits. beta12orEarlier + This can involve characterisation of the underlying quantitative trait loci (QTLs) or nucleotides (QTNs). @@ -38152,7 +38273,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Haplotype inference Infer haplotypes, either alleles at multiple loci that are transmitted together on the same chromosome, or a set of single nucleotide polymorphisms (SNPs) on a single chromatid that are statistically associated. beta12orEarlier - Haplotype inference can help in population genetic studies and the identification of complex disease genes, , and is typically based on aligned single nucleotide polymorphism (SNP) fragments. Haplotype comparison is a useful way to characterize the genetic variation between individuals. An individual's haplotype describes which nucleotide base occurs at each position for a set of common SNPs. Tools might use combinatorial functions (for example parsimony) or a likelihood function or model with optimization such as minimum error correction (MEC) model, expectation-maximization algorithm (EM), genetic algorithm or Markov chain Monte Carlo (MCMC). + Haplotype inference can help in population genetic studies and the identification of complex disease genes, , and is typically based on aligned single nucleotide polymorphism (SNP) fragments. Haplotype comparison is a useful way to characterize the genetic variation between individuals. An individual's haplotype describes which nucleotide base occurs at each position for a set of common SNPs. Tools might use combinatorial functions (for example parsimony) or a likelihood function or model with optimisation such as minimum error correction (MEC) model, expectation-maximisation algorithm (EM), genetic algorithm or Markov chain Monte Carlo (MCMC). Haplotype reconstruction @@ -39062,14 +39183,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Phylogenetic tree construction (from gene frequencies) @@ -39196,14 +39317,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Identify a plausible model of DNA substitution that explains a molecular (DNA or protein) sequence alignment. @@ -40775,14 +40896,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Structure analysis (protein) @@ -40936,14 +41057,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + This is a broad concept and is used a placeholder for other, more specific concepts. @@ -40963,14 +41084,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Analyse known protein secondary structure data. @@ -41158,7 +41279,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Validation beta12orEarlier - Validation and standardisation Quality control Validate some data. @@ -41282,14 +41402,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Predict a network of gene regulation. @@ -41540,14 +41660,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Gene component prediction @@ -41883,13 +42003,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - + - + Simulate molecular (typically protein) conformation using a computational model of physical forces and computer simulation. @@ -42111,7 +42231,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Protein subcellular localization prediction + Protein subcellular localisation prediction @@ -42120,9 +42240,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - The prediction might include subcellular localization (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or export (extracellular proteins) of a protein. - Predict the subcellular localization of a protein sequence. + The prediction might include subcellular localisation (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or export (extracellular proteins) of a protein. Protein targeting prediction + Predict the subcellular localisation of a protein sequence. beta12orEarlier @@ -42168,14 +42288,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Predict the interactions of proteins with other molecules. @@ -42621,14 +42741,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + @@ -42972,14 +43092,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + beta12orEarlier @@ -43026,20 +43146,20 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + - - + + Analyse a body of scientific text (typically a full text article from a scientific journal.) @@ -43072,14 +43192,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + beta12orEarlier @@ -43444,14 +43564,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Features includes functional sites or regions, secondary structure, structural domains and so on. Methods might use fingerprints, motifs, profiles, hidden Markov models, sequence alignment etc to provide a mapping of a query protein sequence to a discriminatory element. This includes methods that search a secondary protein database (Prosite, Blocks, ProDom, Prints, Pfam etc.) to assign a protein sequence(s) to a known protein family or group. @@ -43541,14 +43661,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + @@ -43968,7 +44088,6 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Genome visualisation 1.1 - Genome visualization Visualise, format or render a nucleic acid sequence that is part of (and in context of) a complete genome sequence. Genome rendering Genome browser @@ -44245,11 +44364,11 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp - Variant prioritization + Variant prioritisation - Variant prioritization can be used for example to produce a list of variants responsible for 'knocking out' genes in specific genomes. Methods amino acid substitution, aggregative approaches, probabilistic approach, inheritance and unified likelihood-frameworks. Identify biologically interesting variants by prioritizing individual variants, for example, homozygous variants absent in control genomes. 1.1 + Variant prioritisation can be used for example to produce a list of variants responsible for 'knocking out' genes in specific genomes. Methods amino acid substitution, aggregative approaches, probabilistic approach, inheritance and unified likelihood-frameworks. @@ -44283,7 +44402,7 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Detect large regions in a genome subject to copy-number variation, or other structural variations in genome(s). 1.1 - Methods might involve analysis of whole-genome array comparative genome hybridization or single-nucleotide polymorphism arrays, paired-end mapping of sequencing data, or from analysis of short reads from new sequencing technologies. + Methods might involve analysis of whole-genome array comparative genome hybridisation or single-nucleotide polymorphism arrays, paired-end mapping of sequencing data, or from analysis of short reads from new sequencing technologies. @@ -44348,7 +44467,7 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Methods typically implement some statistical model for hypothesis testing, and methods estimate total copy number, i.e. do not distinguish the two inherited chromosomes quantities (specific copy number). Transcript copy number estimation 1.1 - Estimate the number of copies of loci of particular gene(s) in DNA sequences typically from gene-expression profiling technology based on microarray hybridization-based experiments. For example, estimate copy number (or marker dosage) of a dominant marker in samples from polyploid plant cells or tissues, or chromosomal gains and losses in tumors. + Estimate the number of copies of loci of particular gene(s) in DNA sequences typically from gene-expression profiling technology based on microarray hybridisation-based experiments. For example, estimate copy number (or marker dosage) of a dominant marker in samples from polyploid plant cells or tissues, or chromosomal gains and losses in tumors. @@ -44432,13 +44551,13 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp - + - + @@ -44616,13 +44735,13 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp - + - + 1.4 @@ -44667,14 +44786,14 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp - - + + - - + + Recognition of which format the given data is in. @@ -44689,8 +44808,8 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp The has_input "Data" (data_0006) may cause visualisation or other problems although ontologically correct. But on the other hand it may be useful to distinguish from nullary operations without inputs. - + @@ -44803,11 +44922,11 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp - Standardization and normalization + Standardisation and normalisation - Normalization + Normalisation 1.6 - Standardization + Standardisation Standardize or normalize data. @@ -44911,7 +45030,6 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp 1.7 The analysis of a image (typically a digital image) of some type in order to extract information from it. Image processing - @@ -45389,7 +45507,6 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Visualise images resulting from various types of microscopy. 1.9 - Microscopy image visualisation @@ -45546,20 +45663,20 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp - - + + - - + + - - + + 1.12 @@ -45676,14 +45793,14 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp - - + + - - + + 1.12 @@ -46249,11 +46366,78 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Ancestral reconstruction + Character optimisation 1.15 Ancestral reconstruction is often used to recover possible ancestral character states of ancient, extinct organisms. The extrapolation of empirical characteristics of individuals or populations, backwards in time, to their common ancestors. Character mapping - Character optimization + + + + + + + + + + PTM localisation + + Site localisation of post-translational modifications in peptide or protein mass spectra. + Site localisation + 1.16 + PTM scoring + + + + + + + + + + Service management + + 1.16 + Operations concerning the handling and use of other tools. + + + + + + + + + + Service discovery + + 1.16 + An operation supporting the browsing or discovery of other tools and services. + + + + + + + + + + Service composition + + 1.16 + An operation supporting the aggregation of other services (at least two) into a funtional unit, for the automation of some task. + + + + + + + + + + Service invocation + + 1.16 + An operation supporting the calling (invocation) of other tools and services. @@ -46874,12 +47058,12 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp - Protein targeting and localization + Protein targeting and localisation + Protein localisation Protein targeting Protein sorting - The study of how proteins are transported within and without the cell, including signal peptides, protein subcellular localization and export. - Protein localization + The study of how proteins are transported within and without the cell, including signal peptides, protein subcellular localisation and export. beta12orEarlier @@ -48207,13 +48391,13 @@ long terminal repeats (LTRs); sequences (typically retroviral) directly repeated Probes and primers Probes + Molecular probes (e.g. a peptide probe or DNA microarray probe) or PCR primers and hybridisation oligos in a nucleic acid sequence. + This includes the design of primers for PCR and DNA amplification or the design of molecular probes. http://purl.bioontology.org/ontology/MSH/D015335 Primers true beta12orEarlier - Molecular probes (e.g. a peptide probe or DNA microarray probe) or PCR primers and hybridization oligos in a nucleic acid sequence. - @@ -48964,7 +49148,7 @@ positional features such as functional sites in nucleotide sequences. true 1.13 - PCR primers and hybridization oligos in a nucleic acid sequence. + PCR primers and hybridisation oligos in a nucleic acid sequence. beta12orEarlier @@ -50470,8 +50654,8 @@ positional features such as functional sites in nucleotide sequences.This includes ribosome binding sites (Shine-Dalgarno sequence in prokaryotes), restriction enzyme recognition sites (restriction sites) etc. Restriction sites Ribosome binding sites + This includes sites involved with DNA replication and recombination. This includes binding sites for initiation of replication (origin of replication), regions where transfer is initiated during the conjugation or mobilisation (origin of transfer), starting sites for DNA duplication (origin of replication) and regions which are eliminated through any of kind of recombination. Also nucleosome exclusion regions, i.e. specific patterns or regions which exclude nucleosomes (the basic structural units of eukaryotic chromatin which play a significant role in regulating gene expression). Scaffold-attachment region - This includes sites involved with DNA replication and recombination. This includes binding sites for initiation of replication (origin of replication), regions where transfer is initiated during the conjugation or mobilization (origin of transfer), starting sites for DNA duplication (origin of replication) and regions which are eliminated through any of kind of recombination. Also nucleosome exclusion regions, i.e. specific patterns or regions which exclude nucleosomes (the basic structural units of eukaryotic chromatin which play a significant role in regulating gene expression). Nucleic acids binding to some other molecule. Matrix/scaffold attachment region @@ -50546,8 +50730,8 @@ positional features such as functional sites in nucleotide sequences. Sequencing - Amplicon sequencing is the ultra-deep sequencing of PCR products (amplicons), usually for the purpose of efficient genetic variant identification and characterization in specific genomic regions. Resequencing + Amplicon sequencing is the ultra-deep sequencing of PCR products (amplicons), usually for the purpose of efficient genetic variant identification and characterisation in specific genomic regions. true http://purl.bioontology.org/ontology/MSH/D059014 Chromosome walking